Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory von Chaisson, Mark J, Tesler, Glenn

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Genetic variation and the de novo assembly of human genomes von Chaisson, Mark J. P., Wilson, Richard K., Eichler, Evan E.

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lra: A long read aligner for sequences and contigs von Ren, Jingwen, Chaisson, Mark J P

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Resolving the complexity of the human genome using single-molecule sequencing von Chaisson, Mark J. P., Huddleston, John, Dennis, Megan Y., Sudmant, Peter H., Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M., Stamatoyannopoulos, John A., Hunkapiller, Michael W., Korlach, Jonas, Eichler, Evan E.

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vamos: variable-number tandem repeats annotation using efficient motif sets von Ren, Jingwen, Gu, Bida, Chaisson, Mark J P

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TT-Mars: structural variants assessment based on haplotype-resolved assemblies von Yang, Jianzhi, Chaisson, Mark J P

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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads von Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O., Eichler, Evan E., Marschall, Tobias

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Discovery and genotyping of structural variation from long-read haploid genome sequence data von Huddleston, John, Chaisson, Mark J P, Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A, Munson, Katherine M, Kronenberg, Zev N, Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K, Eichler, Evan E

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The Human Pangenome Project: a global resource to map genomic diversity von Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David

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High-resolution comparative analysis of great ape genomes von Kronenberg, Zev N, Fiddes, Ian T, Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S, Underwood, Jason G, Nelson, Bradley J, Chaisson, Mark J P, Dougherty, Max L, Munson, Katherine M, Hastie, Alex R, Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E, Sorensen, Melanie, Baker, Carl, Fulton, Robert S, Armstrong, Joel, Graves-Lindsay, Tina A, Denli, Ahmet M, Hoppe, Emma R, Hsieh, PingHsun, Hill, Christopher M, Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T, Dutcher, Susan K, Gage, Fred H, Warren, Wesley C, Shendure, Jay, Haussler, David, Schneider, Valerie A, Cao, Han, Ventura, Mario, Wilson, Richard K, Paten, Benedict, Pollen, Alex, Eichler, Evan E

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs von Lu, Tsung-Yu, Chaisson, Mark J. P.

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Long-read sequence assembly of the gorilla genome von Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.

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An integrated map of structural variation in 2,504 human genomes von Sudmant, Peter H., Rausch, Tobias, Gardner, Eugene J., Handsaker, Robert E., Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Hsi-Yang Fritz, Markus, Konkel, Miriam K., Malhotra, Ankit, Stütz, Adrian M., Shi, Xinghua, Paolo Casale, Francesco, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark J. P., Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo Y. K., Jasmine Mu, Xinmeng, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M., Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A., Marth, Gabor, Mason, Christopher E., Menelaou, Androniki, Muzny, Donna M., Nelson, Bradley J., Noor, Amina, Parrish, Nicholas F., Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E., Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A., Untergasser, Andreas, Walker, Jerilyn A., Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A., McCarroll, Steven A., Mills, Ryan E., Gerstein, Mark B., Bashir, Ali, Stegle, Oliver, Devine, Scott E., Lee, Charles, Eichler, Evan E., Korbel, Jan O.

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The motif composition of variable number tandem repeats impacts gene expression von Lu, Tsung-Yu, Smaruj, Paulina N, Fudenberg, Geoffrey, Mancuso, Nicholas, Chaisson, Mark J P

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HQAlign: aligning nanopore reads for SV detection using current-level modeling von Joshi, Dhaivat, Diggavi, Suhas, Chaisson, Mark J P, Kannan, Sreeram

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Long-read sequence and assembly of segmental duplications von Vollger, Mitchell R., Dishuck, Philip C., Sorensen, Melanie, Welch, AnneMarie E., Dang, Vy, Dougherty, Max L., Graves-Lindsay, Tina A., Wilson, Richard K., Chaisson, Mark J. P., Eichler, Evan E.

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Short read fragment assembly of bacterial genomes von Chaisson, Mark J, Pevzner, Pavel A

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Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies von Zhao, Xuefang, Collins, Ryan L., Lee, Wan-Ping, Weber, Alexandra M., Jun, Yukyung, Zhu, Qihui, Weisburd, Ben, Huang, Yongqing, Audano, Peter A., Wang, Harold, Walker, Mark, Lowther, Chelsea, Fu, Jack, Gerstein, Mark B., Devine, Scott E., Marschall, Tobias, Korbel, Jan O., Eichler, Evan E., Chaisson, Mark J.P., Lee, Charles, Mills, Ryan E., Brand, Harrison, Talkowski, Michael E.

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Assembly of long error-prone reads using de Bruijn graphs von Lin, Yu, Yuan, Jeffrey, Kolmogorov, Mikhail, Shen, Max W., Chaisson, Mark, Pevzner, Pavel A.

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STAR: ultrafast universal RNA-seq aligner von Dobin, Alexander, Davis, Carrie A, Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R

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